createSampleList: Creating sample list to run mcapply parallel

View source: R/createSampleListFunction.R

createSampleListR Documentation

Creating sample list to run mcapply parallel

Description

Function to create sample list to run mcapply parallel

Usage

createSampleList(samples, reads_folder, column, program, libraryType, fileType, fromSTAR = FALSE)

Arguments

samples

Character. The filename of the sample file. Default samples.txt.

reads_folder

Character. Directory where the raw sequence data is stored. Default 00-Fastq.

column

Character. Column name from the sample sheet to use as read folder names. Default SAMPLE_ID

program

Character. The program to be used. Available 'trimmomatic', 'star', 'Hisat2', 'htseq', 'featurecount', 'bowtie', 'samtools' or 'bwa'

libraryType

Character. The library type to use. Available: 'pairEnd' or 'singleEnd'.

fileType

Character. The file type to use. Available: 'bam' or 'sam'.

fromSTAR

Logical. Wheter to use samples from STAR in FeatureCouts

Details

December 2021

Author(s)

Haniel Cedraz


hanielcedraz/baqcomPackage documentation built on June 14, 2022, 12:25 a.m.